The sales rep where I bought my new iphone set up the transfer data from my old phone to the new phone however some of my apps did not transfer am I able to run the data transfer again without causing any problems?

What apps are missing? Apps get downloaded directly from the App Store, so you can just manually download them on the new phone.

If the apps are no longer available in the store, you cannot download them from the old phone. You will no longer be able to access those apps.

~Lyssa

To Add: go into your App Store on the new iPhone, click on your icon at top right, then under Purchased, you can see any Apps will available, to download again to the new device. Nothing incorrect happened. Your data should all still be there after you log back into each app.